Dear Chimera users, I want to calculate H bonds between the ligand of my protein and its nearby residues. Could you give any suggestions on how to select this residues and calculate H bonds between them and the ligand? Kind regards,Kloe
Hi Kloe, I mentioned the FindHBond tool in my previous reply to you. Did you try it? <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-December/015299.html>
Open tools from the Chimera Tools menu, for example:
Tools… Structure Analysis… FindHBond Tools… Structure Analysis… Find Clashes/Contacts
If you show a tool and click the Help button on that tool, it will explain the options. Also, you should go through the “Structure Analysis and Comparison” tutorial, which includes FIndHBond and some other things for looking at ligand-receptor interactions <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 29, 2018, at 3:43 PM, kloe brathon <kloebrathon@yahoo.com> wrote:
Dear Chimera users, I want to calculate H bonds between the ligand of my protein and its nearby residues. Could you give any suggestions on how to select this residues and calculate H bonds between them and the ligand? Kind regards, Kloe
Hello, Thank you for your reply!I tried that, but it gives me all the H bonds of the structure and its a very complicated image. I was interested only in H bonds of ligands with its nearby residues. Maybe I should write any specificity on the script. Also, I am comparing the ligand bound and unbound form of two proteins. I used the Blast option that you had mentioned in a previous discussion. It worked perfectly to find a molecule that did not have the ligand, but now I am not sure on what can I do to compare their stabilities.I tried minimize option but it dd not give any difference to my protein. Regards,Kloe Happy New Year 2019! 30 Aralık 2018 Pazar 21:32:32 GMT+3 tarihinde, Elaine Meng <meng@cgl.ucsf.edu>şunu yazdı: Hi Kloe, I mentioned the FindHBond tool in my previous reply to you. Did you try it? <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-December/015299.html>
Open tools from the Chimera Tools menu, for example:
Tools… Structure Analysis… FindHBond Tools… Structure Analysis… Find Clashes/Contacts
If you show a tool and click the Help button on that tool, it will explain the options. Also, you should go through the “Structure Analysis and Comparison” tutorial, which includes FIndHBond and some other things for looking at ligand-receptor interactions <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 29, 2018, at 3:43 PM, kloe brathon <kloebrathon@yahoo.com> wrote:
Dear Chimera users, I want to calculate H bonds between the ligand of my protein and its nearby residues. Could you give any suggestions on how to select this residues and calculate H bonds between them and the ligand? Kind regards, Kloe
Hi Kloe, Both of these things I told you before. (1) Chimera does not calculate stability values; you have to use your own chemical intuition. <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-December/015297.html> (2) The tutorial I recommended in the previous reply includes an example of calculating only the H-bonds to the ligand. <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-December/015310.html> Elaine
On Dec 31, 2018, at 11:16 AM, kloe brathon <kloebrathon@yahoo.com> wrote:
Hello,
Thank you for your reply! I tried that, but it gives me all the H bonds of the structure and its a very complicated image. I was interested only in H bonds of ligands with its nearby residues. Maybe I should write any specificity on the script.
Also, I am comparing the ligand bound and unbound form of two proteins. I used the Blast option that you had mentioned in a previous discussion. It worked perfectly to find a molecule that did not have the ligand, but now I am not sure on what can I do to compare their stabilities. I tried minimize option but it dd not give any difference to my protein.
Regards, Kloe
Happy New Year 2019!
30 Aralık 2018 Pazar 21:32:32 GMT+3 tarihinde, Elaine Meng <meng@cgl.ucsf.edu>şunu yazdı:
Hi Kloe, I mentioned the FindHBond tool in my previous reply to you. Did you try it?
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-December/015299.html>
Open tools from the Chimera Tools menu, for example:
Tools… Structure Analysis… FindHBond Tools… Structure Analysis… Find Clashes/Contacts
If you show a tool and click the Help button on that tool, it will explain the options.
Also, you should go through the “Structure Analysis and Comparison” tutorial, which includes FIndHBond and some other things for looking at ligand-receptor interactions
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 29, 2018, at 3:43 PM, kloe brathon <kloebrathon@yahoo.com> wrote:
Dear Chimera users, I want to calculate H bonds between the ligand of my protein and its nearby residues. Could you give any suggestions on how to select this residues and calculate H bonds between them and the ligand? Kind regards, Kloe
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kloe brathon